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Abstract
Ruminants (Ruminantia) are among the most successful herbivorous mammals, exhibiting wide-ranging morphological and ecological characteristics (such as headgear and multichambered stomach) and including various key livestock species (e.g., cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.
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Affiliation(s)
- Bao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
| | - Le Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China, E-mail:chen_
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:.,Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, China
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152
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Yao YG, Shen H. From our roots, we grow. Zool Res 2019; 40:471-475. [PMID: 31631589 PMCID: PMC6822935 DOI: 10.24272/j.issn.2095-8137.2019.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/26/2019] [Indexed: 11/07/2022] Open
Abstract
Located at the head of the Indo-Burma biodiversity hotspot, the Kunming Institute of Zoology (KIZ), Chinese Academy of Sciences (CAS), serves as China's main center for research into the diverse animal and ecological resources of southwestern China, Eastern Himalayas, and Southeast Asia. As of October 2019, it has been 60 years since the inception of KIZ. Since 1959, strong roots have been laid down by generations of researchers, allowing KIZ to grow and evolve into a comprehensive research institution renowned for its remarkable achievements in evolutionary mechanisms of animal biodiversity, animal resources protection, and sustainable utilization. It is now recognized as "a major powerhouse in evolutionary biology research in China" and is"establishing itself in the world stage" (Overseas Experts Review Committee, organized by the Bureau of Development Planning, CAS, during international evaluation in 2014).To celebrate the 60th anniversary of KIZ and the 70th anniversary of CAS, Zoological Research presents this commemorative issue, composed primarily of contributions from KIZ researchers. In addition, it is our great honor to provide here a brief retrospective of the pioneering work undertaken by the earlier scientists at KIZ and recent achievements, which will hopefully serve to motivate and inspire present and future successors.
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Affiliation(s)
- Yong-Gang Yao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Hua Shen
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
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153
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Li R, Fu W, Su R, Tian X, Du D, Zhao Y, Zheng Z, Chen Q, Gao S, Cai Y, Wang X, Li J, Jiang Y. Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome. Front Genet 2019; 10:1169. [PMID: 31803240 PMCID: PMC6874019 DOI: 10.3389/fgene.2019.01169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/23/2019] [Indexed: 01/08/2023] Open
Abstract
It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock. However, the rich diversity of worldwide goat breeds indicates that a genome from one individual would be insufficient to represent the whole genomic contents of goats. By comparing nine de novo assemblies from seven sibling species of domestic goat with ARS1 and using resequencing and transcriptome data from goats for verification, we identified a total of 38.3 Mb sequences that were absent in ARS1. The pan-sequences contain genic fractions with considerable expression. Using the pan-genome (ARS1 together with the pan-sequences) as a reference genome, variation calling efficacy can be appreciably improved. A total of 56,657 spurious SNPs per individual were repressed and 24,414 novel SNPs per individual on average were recovered as a result of better reads mapping quality. The transcriptomic mapping rate was also increased by ∼1.15%. Our study demonstrated that comparing de novo assemblies from closely related species is an efficient and reliable strategy for finding missing sequences from the reference genome and could be applicable to other species. Pan-genome can serve as an improved reference genome in animals for a better exploration of the underlying genomic variations and could increase the probability of finding genotype-phenotype associations assessed by a comprehensive variation database containing much more differences between individuals. We have constructed a goat pan-genome web interface for data visualization (http://animal.nwsuaf.edu.cn/panGoat).
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Affiliation(s)
- Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomeng Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Duo Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yue Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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154
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Sparks AM, Watt K, Sinclair R, Pilkington JG, Pemberton JM, McNeilly TN, Nussey DH, Johnston SE. The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries). PLoS Genet 2019; 15:e1008461. [PMID: 31697674 PMCID: PMC6863570 DOI: 10.1371/journal.pgen.1008461] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 11/19/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of St Kilda, an unmanaged population of sheep infected with strongyle gastrointestinal nematodes. We assayed IgA, IgE and IgG antibodies against the prevalent nematode Teladorsagia circumcincta in the blood plasma of > 3,000 sheep collected over 26 years. Antibody levels were significantly heritable (h2 = 0.21 to 0.57) and highly stable over an individual’s lifespan. IgA levels were strongly associated with a region on chromosome 24 explaining 21.1% and 24.5% of heritable variation in lambs and adults, respectively. This region was adjacent to two candidate loci, Class II Major Histocompatibility Complex Transactivator (CIITA) and C-Type Lectin Domain Containing 16A (CLEC16A). Lamb IgA levels were also associated with the immunoglobulin heavy constant loci (IGH) complex, and adult IgE levels and lamb IgA and IgG levels were associated with the major histocompatibility complex (MHC). This study provides evidence of high heritability of a complex immunological trait under natural conditions and provides the first evidence from a genome-wide study that large effect genes located outside the MHC region exist for immune traits in the wild. Understanding how immune responses vary in natural populations can give an insight into how infection affects the ability of hosts and parasites to survive and reproduce, and how this drives evolutionary and ecological dynamics. Yet, very little is known about how immune responses vary over an individual’s lifetime and how genes contribute to this variation under natural conditions. Our study investigates the genetic architecture of variation in three antibody types, IgA, IgE and IgG in a wild population of Soay sheep on the St Kilda archipelago in North-West Scotland. Using data collected over 26 years, we show that antibody levels have a heritable basis in lambs and adults and are stable over an individual’s lifetime. We also identify several genomic regions with large effects on immune responses. Our study offers the first insights into the genetic control of immunity in a wild population, which is essential to understand how immune profiles vary in challenging natural conditions and how natural selection maintains genetic variation in complex immune traits.
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Affiliation(s)
- Alexandra M. Sparks
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
| | - Kathryn Watt
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rona Sinclair
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jill G. Pilkington
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Josephine M. Pemberton
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, United Kingdom
| | - Daniel H. Nussey
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan E. Johnston
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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155
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Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Mol Ecol Resour 2019; 19:1497-1515. [PMID: 31359622 PMCID: PMC7115901 DOI: 10.1111/1755-0998.13070] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 06/30/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.
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Affiliation(s)
- Badr Benjelloun
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Frédéric Boyer
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Wahid Zamani
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, 46417-76489 Noor, Mazandaran, Iran
| | - Stefan Engelen
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Adriana Alberti
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Florian J. Alberto
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Mohamed BenBati
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Mustapha Ibnelbachyr
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Mouad Chentouf
- National Institute of Agronomic Research (INRA Maroc), CRRA Tangier, 90010 Tangier, Morocco
| | - Abdelmajid Bechchari
- National Institute of Agronomic Research (INRA Maroc), CRRA Oujda, 60000 Oujda, Morocco
| | - Hamid R. Rezaei
- Department of Environmental Sci, Gorgan University of Agricultural Sciences & Natural Resources, 41996-13776 Gorgan, Iran
| | - Saeid Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, 49138-15749 Guilan, Iran
| | - Alessandra Stella
- PTP Science Park, Bioinformatics Unit, Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Abdelkader Chikhi
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pierre Taberlet
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Pompanon
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
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156
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McHugo GP, Browett S, Randhawa IAS, Howard DJ, Mullen MP, Richardson IW, Park SDE, Magee DA, Scraggs E, Dover MJ, Correia CN, Hanrahan JP, MacHugh DE. A Population Genomics Analysis of the Native Irish Galway Sheep Breed. Front Genet 2019; 10:927. [PMID: 31649720 PMCID: PMC6792165 DOI: 10.3389/fgene.2019.00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022] Open
Abstract
The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in production and health traits.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sam Browett
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Imtiaz A S Randhawa
- Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Dawn J Howard
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - Michael P Mullen
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | | | | | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Erik Scraggs
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - James P Hanrahan
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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157
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Genetic Variability in the Loci of FABP4, PPARγ and SCD Genes of Sheep Breeds Raised for Different Purposes. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The present study was undertaken to analyse the genetic variation in coding sequences, splicing sites and regulatory sequences of FABP4, PPARγ and SCD genes in five breeds of sheep raised in Poland with different purposes: meat (Suffolk, Ile de France), dairy/prolific (Olkuska sheep, Kołuda) and primitive breeds (Polish Mountain Sheep). To identify genetic variability HRM-PCR, sequencing and PCR-RFLP method were used. Determining the genetic structure of the mentioned genes revealed six SNPs: FABP4 – c.73 + 13A>T and c.348 + 85G>A, PPARγ – c.391 – 66C>T (c.481 – 66C>T) and c.529 + 27G>C (c.619 + 27G>C), SCD – c.*945G>A and c.*1116A>G. For the c.*1116A>G SNP, a potential association with specific sheep body type and breeding purpose was found. In turn, the substitution c.*945G>A located in the regulatory region of the 3'-UTR of the Ovis aries SCD gene was identified for the first time. Based on the relationship demonstrated between sheep body constitution and productive type (dairy, meat) and the polymorphism of the SCD gene, further research is needed. The correlation between c.*1116A>G polymorphism and growth rate, slaughter and carcass value as well as meat quality of lambs needs to be studied in more detail. Such studies may lead to more effective selection processes in sheep breeding in the future.
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158
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Salavati M, Bush SJ, Palma-Vera S, McCulloch MEB, Hume DA, Clark EL. Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep. Front Genet 2019; 10:863. [PMID: 31608110 PMCID: PMC6761296 DOI: 10.3389/fgene.2019.00863] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Pervasive allelic variation at both gene and single nucleotide level (SNV) between individuals is commonly associated with complex traits in humans and animals. Allele-specific expression (ASE) analysis, using RNA-Seq, can provide a detailed annotation of allelic imbalance and infer the existence of cis-acting transcriptional regulation. However, variant detection in RNA-Seq data is compromised by biased mapping of reads to the reference DNA sequence. In this manuscript, we describe an unbiased standardized computational pipeline for allele-specific expression analysis using RNA-Seq data, which we have adapted and developed using tools available under open license. The analysis pipeline we present is designed to minimize reference bias while providing accurate profiling of allele-specific expression across tissues and cell types. Using this methodology, we were able to profile pervasive allelic imbalance across tissues and cell types, at both the gene and SNV level, in Texel×Scottish Blackface sheep, using the sheep gene expression atlas data set. ASE profiles were pervasive in each sheep and across all tissue types investigated. However, ASE profiles shared across tissues were limited, and instead, they tended to be highly tissue-specific. These tissue-specific ASE profiles may underlie the expression of economically important traits and could be utilized as weighted SNVs, for example, to improve the accuracy of genomic selection in breeding programs for sheep. An additional benefit of the pipeline is that it does not require parental genotypes and can therefore be applied to other RNA-Seq data sets for livestock, including those available on the Functional Annotation of Animal Genomes (FAANG) data portal. This study is the first global characterization of moderate to extreme ASE in tissues and cell types from sheep. We have applied a robust methodology for ASE profiling to provide both a novel analysis of the multi-dimensional sheep gene expression atlas data set and a foundation for identifying the regulatory and expressed elements of the genome that are driving complex traits in livestock.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Sergio Palma-Vera
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Reproductive Biology, Dummerstorf, Germany
| | - Mary E. B. McCulloch
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Emily L. Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
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159
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Wang D, Chen X, Zhang X, Li J, Yi Y, Bian C, Shi Q, Lin H, Li S, Zhang Y, You X. Whole Genome Sequencing of the Giant Grouper ( Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes. Mar Drugs 2019; 17:E503. [PMID: 31466296 PMCID: PMC6780625 DOI: 10.3390/md17090503] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 12/25/2022] Open
Abstract
Giant groupers, the largest grouper type in the world, are of economic importance in marine aquaculture for their rapid growth. At the same time, bacterial and viral diseases have become the main threats to the grouper industry. Here, we report a high-quality genome of a giant grouper sequenced by an Illumina HiSeq X-Ten and PacBio Bioscience Sequel platform. A total of 254 putative antimicrobial peptide (AMP) genes were identified, which can be divided into 34 classes according to the annotation of the Antimicrobial Peptides Database (APD3). Their locations in pseudochromosomes were also determined. Thrombin-, lectin-, and scolopendin-derived putative AMPs were the three largest parts. In addition, expressions of putative AMPs were measured by our transcriptome data. Two putative AMP genes (gapdh1 and gapdh2) were involved in glycolysis, which had extremely high expression levels in giant grouper muscle. As it has been reported that AMPs inhibit the growth of a broad spectrum of microbes and participate in regulating innate and adaptive immune responses, genome sequencing of this study provides a comprehensive cataloging of putative AMPs of groupers, supporting antimicrobial research and aquaculture therapy. These genomic resources will be beneficial to further molecular breeding of this economically important fish.
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Affiliation(s)
- Dengdong Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiyang Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yunhai Yi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
- Zhanjiang Bay Laboratory, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
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160
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Gene expression analysis of ovine prepubertal testicular tissue vitrified with a novel cryodevice (E.Vit). J Assist Reprod Genet 2019; 36:2145-2154. [PMID: 31414315 DOI: 10.1007/s10815-019-01559-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Testicular tissue cryopreservation prior to gonadotoxic therapies is a method to preserve fertility in children. However, the technique still requires development, especially when the tissue is immature and rather susceptible to stress derived from in vitro manipulation. This study aimed to investigate the effects of vitrification with a new cryodevice (E.Vit) on cell membrane integrity and gene expression of prepubertal testicular tissue in the ovine model. METHODS Pieces of immature testicular tissue (1 mm3) were inserted into "E.Vit" devices and vitrified with a two-step protocol. After warming, tissues were cultured in vitro and cell membrane integrity was assessed after 0, 2, and 24 h by trypan blue exclusion test. Controls consisted of non-vitrified tissue analyzed after 0, 2, and 24 h in vitro culture (IVC). Expression of genes involved in transcriptional stress response (BAX, SOD1, CIRBP, HSP90AB1), cell proliferation (KIF11), and germ- (ZBDB16, TERT, POU5F1, KIT) and somatic- (AR, FSHR, STAR) cell specific markers was evaluated 2 and 24 h after warming. RESULTS Post-warming trypan blue staining showed the survival of most cells, although membrane integrity immediately after warming (66.00% ± 4.73) or after 2 h IVC (59.67% ± 4.18) was significantly lower than controls (C0h 89.67% ± 1.45). Extended post-warming IVC (24 h) caused an additional decrease to 31% ± 3.46 (P < 0.05). Germ- and somatic-cell specific markers showed the survival of both cell types after cryopreservation and IVC. All genes were affected by cryopreservation and/or IVC, and moderate stress conditions were indicated by transcriptional stress response. CONCLUSIONS Vitrification with the cryodevice E.Vit is a promising strategy to cryopreserve prepubertal testicular tissue.
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161
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Yuan Z, Li W, Li F, Yue X. Selection signature analysis reveals genes underlying sheep milking performance. Arch Anim Breed 2019; 62:501-508. [PMID: 31807661 PMCID: PMC6859915 DOI: 10.5194/aab-62-501-2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/15/2019] [Indexed: 11/30/2022] Open
Abstract
Sheep milk is the most important feed resource for newborn lambs and an important food resource for humans. Sheep milk production and ingredients are influenced by genetic and environmental factors. In this study, we implemented selection signature analysis using Illumina Ovine SNP50 BeadChip data of 78 meat Lacaune and 103 milk Lacaune sheep, which have similar genetic backgrounds, from the Sheep HapMap project to identify candidate genes related to ovine milk traits. Since different methods can detect different variation types and complement each other, we used a haplotype-based method (hapFLK) to implement selection signature analysis. The results revealed six selection signature regions showing signs of being selected ( P < 0.001 ): chromosomes 1, 2, 3, 6, 13 and 18. In addition, 38 quantitative trait loci (QTLs) related to sheep milk performance were identified in selection signature regions, which contain 334 candidate genes. Of those, SUCNR1 (succinate receptor 1) and PPARGC1A (PPARG coactivator 1 alpha) may be the most significant genes that affect sheep milking performance, which supply a significant indication for future studies to investigate candidate genes that play an important role in milk production and quality.
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Affiliation(s)
- Zehu Yuan
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural
Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou
University, Lanzhou, 730020, P. R. China
| | - Wanhong Li
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural
Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou
University, Lanzhou, 730020, P. R. China
| | - Fadi Li
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural
Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou
University, Lanzhou, 730020, P. R. China
- Engineering Laboratory of Sheep Breeding and Reproduction
Biotechnology in Gansu Province, Minqin, 733300, P. R. China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural
Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou
University, Lanzhou, 730020, P. R. China
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162
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Lopes-Marques M, Machado AM, Alves LQ, Fonseca MM, Barbosa S, Sinding MHS, Rasmussen MH, Iversen MR, Frost Bertelsen M, Campos PF, da Fonseca R, Ruivo R, Castro LFC. Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea. Mol Biol Evol 2019; 36:1270-1280. [PMID: 30895322 PMCID: PMC6526905 DOI: 10.1093/molbev/msz068] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands (SGs), for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity, and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol, and squalene. Remarkably, SGs are absent in a few mammalian lineages, including the iconic Cetacea. We investigated the evolution of the key molecular components responsible for skin sebum production: Dgat2l6, Awat1, Awat2, Elovl3, Mogat3, and Fabp9. We show that all analyzed genes have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Transcriptomic analysis, including a novel skin transcriptome from blue whale, supports gene inactivation. The conserved mutational pattern found in most analyzed genes, indicates that pseudogenization events took place prior to the diversification of modern Cetacea lineages. Genome and skin transcriptome analysis of the common hippopotamus highlighted the convergent loss of a subset of sebum-producing genes, notably Awat1 and Mogat3. Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.
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Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - André M Machado
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Susana Barbosa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | | | | | | | | | - Paula F Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
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163
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Attwood GT, Wakelin SA, Leahy SC, Rowe S, Clarke S, Chapman DF, Muirhead R, Jacobs JME. Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture. Front Nutr 2019; 6:107. [PMID: 31380386 PMCID: PMC6646666 DOI: 10.3389/fnut.2019.00107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022] Open
Abstract
The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals' rumens. Each of these components has an associated microbiome, and these have traditionally been viewed as distinct ecosystems. However, these microbiomes operate under similar ecological principles and are connected via water, energy flows, and the carbon and nitrogen nutrient cycles. Here, we summarize the microbiome research that has been done in each of these three environments (soils, forage plants, animals' rumen) and investigate what additional benefits may be possible through understanding the interactions between the various microbiomes. The challenge for future research is to enhance microbiome function by appropriate matching of plant and animal genotypes with the environment to improve the output and environmental sustainability of pastoral agriculture.
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Affiliation(s)
| | | | | | - Suzanne Rowe
- Animal Science, AgResearch, Invermay, New Zealand
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164
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165
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Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 2019; 364:364/6446/eaav6202. [DOI: 10.1126/science.aav6202] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/16/2019] [Indexed: 12/17/2022]
Abstract
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
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166
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Li C, Chen L, Liu X, Shi X, Guo Y, Huang R, Nie F, Zheng C, Zhang C, Ma RZ. A high-density BAC physical map covering the entire MHC region of addax antelope genome. BMC Genomics 2019; 20:479. [PMID: 31185912 PMCID: PMC6558854 DOI: 10.1186/s12864-019-5790-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/10/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is available for any of the wild ruminant species in the world. RESULTS The high-density physical map is composed of two contigs of 47 overlapping bacterial artificial chromosome (BAC) clones, with an average of 115 Kb for each BAC, covering the entire addax MHC genome. The first contig has 40 overlapping BAC clones covering an approximately 2.9 Mb region of MHC class I, class III, and class IIa, and the second contig has 7 BAC clones covering an approximately 500 Kb genomic region that harbours MHC class IIb. The relative position of each BAC corresponding to the MHC sequence was determined by comparative mapping using PCR screening of the BAC library of 192,000 clones, and the order of BACs was determined by DNA fingerprinting. The overlaps of neighboring BACs were cross-verified by both BAC-end sequencing and co-amplification of identical PCR fragments within the overlapped region, with their identities further confirmed by DNA sequencing. CONCLUSIONS We report here the successful construction of a high-quality physical map for the addax MHC region using BACs and comparative mapping. The addax MHC physical map we constructed showed one gap of approximately 18 Mb formed by an ancient autosomal inversion that divided the MHC class II into IIa and IIb. The autosomal inversion provides compelling evidence that the MHC organizations in all of the ruminant species are relatively conserved.
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Affiliation(s)
- Chaokun Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, S2-316 Building #2, West Beichen Road, Chaoyang District, Beijing, 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longxin Chen
- Zhengzhou Key Laboratory of Molecular Biology, Zhengzhou Normal University, Zhengzhou, 450044, China
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Xiaoqian Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, S2-316 Building #2, West Beichen Road, Chaoyang District, Beijing, 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Guo
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, S2-316 Building #2, West Beichen Road, Chaoyang District, Beijing, 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, S2-316 Building #2, West Beichen Road, Chaoyang District, Beijing, 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangyuan Nie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, S2-316 Building #2, West Beichen Road, Chaoyang District, Beijing, 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changming Zheng
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China.
- Beijing Zoo, No. 137 West straight door Avenue, Xicheng District, Beijing, 100032, China.
| | - Runlin Z Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, S2-316 Building #2, West Beichen Road, Chaoyang District, Beijing, 100101, China.
- Zhengzhou Key Laboratory of Molecular Biology, Zhengzhou Normal University, Zhengzhou, 450044, China.
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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167
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Ming Y, Jian J, Yu X, Wang J, Liu W. The genome resources for conservation of Indo-Pacific humpback dolphin, Sousa chinensis. Sci Data 2019; 6:68. [PMID: 31118413 PMCID: PMC6531461 DOI: 10.1038/s41597-019-0078-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/16/2019] [Indexed: 11/24/2022] Open
Abstract
The Indo-Pacific humpback dolphin (Sousa chinensis), is a threatened marine mammal and belongs to the First Order of the National Key Protected Wild Aquatic Animals List in China. However, limited genomic information is available for studies of its population genetics and biological conservation. Here, we have assembled a genomic sequence of this species using a whole genome shotgun (WGS) sequencing strategy after a pilot low coverage genome survey. The total assembled genome size was 2.34 Gb: with a contig N50 of 67 kb and a scaffold N50 of 9 Mb (107.6-fold sequencing coverage). The S. chinensis genome contained 24,640 predicted protein-coding genes and had approximately 37% repeated sequences. The completeness of the genome assembly was evaluated by benchmarking universal single copy orthologous genes (BUSCOs): 94.3% of a total 4,104 expected mammalian genes were identified as complete, and 2.3% were identified as fragmented. This newly produced high-quality assembly and annotation of the genome will greatly promote the future studies of the genetic diversity, conservation and evolution.
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Affiliation(s)
- Yao Ming
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Xueying Yu
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China
| | - Jingzhen Wang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China.
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China.
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168
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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169
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Zhang T, Gao H, Sahana G, Zan Y, Fan H, Liu J, Shi L, Wang H, Du L, Wang L, Zhao F. Genome-wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep. J Anim Breed Genet 2019; 136:362-370. [PMID: 31045295 DOI: 10.1111/jbg.12402] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
Abstract
Fat-tailed sheep have a unique characteristic of depositing fat in their tails. In the present study, we conducted genome-wide association studies (GWAS) on traits related to tail fat deposition and body size in the Hulun Buir sheep. A total number of 300 individuals belonging to two fat-tailed lines of the Hulun Buir sheep breed genotyped with the Ovine Infinium HD SNP BeadChip were included in the current study. Two mixed models, one for continuous and one for binary phenotypic traits, were employed to analyse ten traits, that is, body length (BL), body height (BH), chest girth (CG), tail length (TL), tail width (TW), tail circumference (TC), carcass weight (CW), tail fat weight (TF), ratio of CW to TF (RCT) and tail type (TT). We identified 7, 6, 7, 2, 10 and 1 SNPs significantly associated with traits TF, CW, RCT, TW, TT and CG, respectively. Their associated genomic regions harboured 42 positional candidate genes. Out of them, 13 candidate genes including SMURF2, FBF1, DTNBP1, SETD7 and RBM11 have been associated with fat metabolism in sheep. The RBM11 gene has already been identified in a previous study on signatures of selection in this specific sheep population. Two more genes, that is, SMARCA5 and GAB1 were associated with body size in sheep. The present study has identified candidate genes that might be implicated in tail fat deposition and body size in sheep.
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Affiliation(s)
- Tongyu Zhang
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongding Gao
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Yanjun Zan
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hongying Fan
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaxin Liu
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liangyu Shi
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Wang
- Beijing Compass Biotechnology Co., Ltd, Beijing, China
| | - Lixin Du
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuping Zhao
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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170
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Posbergh CJ, Thonney ML, Huson HJ. Genomic Approaches Identify Novel Gene Associations with Out of Season Lambing in Sheep. J Hered 2019; 110:577-586. [DOI: 10.1093/jhered/esz014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
Sheep are seasonally polyestrous, traditionally breeding when the day length shortens in the autumn. The changing photoperiod stimulates reproductive hormones through a series of chemical pathways, ultimately leading to cyclicity. Some breeds of sheep, such as the Polypay and Dorset, have been selected for reduced seasonality and can lamb year-round. Despite this selection, there is still variation within these breeds in the ability to lamb out of season. The identification of out of season lambing quantitative trait loci has the potential to improve genetic progress using genomic selection schemes. Association studies, fixation index (FST), and runs of homozygosity (ROH) were evaluated to identify regions of the genome that influence the ability of ewes to lamb out of season. All analyses used genotypic data from the Illumina Ovine HD beadchip. Genome-wide associations were tested both across breeds in 257 ewes and within the Dorset and Polypay breeds. FST was measured across breeds and between UK and US Dorsets to assess population differences. ROH were estimated in ewes to identify homozygous regions contributing to out of season lambing. Significant associations after multiple testing correction were found through these approaches, leading to the identification of several candidate genes for further study. Genes involved with eye development, reproductive hormones, and neuronal changes were identified as the most promising for influencing the ewe’s ability to lamb year-round. These candidate genes could be advantageous for selection for improved year-round lamb production and provide better insight into the complex regulation of seasonal reproduction.
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Affiliation(s)
| | | | - Heather J Huson
- Department of Animal Science, Cornell University, Ithaca, NY
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171
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Taylor ME, Snelling T, Smith DF, Drickamer K. Absence of a human ortholog of rodent Kupffer cell galactose-binding receptor encoded by the CLEC4f gene. Glycobiology 2019; 29:332-345. [PMID: 30590594 PMCID: PMC6422238 DOI: 10.1093/glycob/cwy113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 01/21/2023] Open
Abstract
The murine CLEC4f gene encodes the Kupffer cell receptor, a galactose-binding receptor containing a C-type carbohydrate-recognition domain. Orthologs have been identified in nearly 100 species. The receptors from rat and mouse have previously been characterized and data presented here show that functional CLEC4f protein is expressed in domestic cattle (Bos taurus). However, the human CLEC4f gene does not encode a functional receptor because a mutation in the splice acceptor site of the final exon prevents appropriate splicing and a missense mutation disrupts the sugar-binding site. Transcriptomic and PCR analysis of transcripts confirms the absence of a spliced transcript containing the final exon and only background levels of transcripts are detected in human tissues. These mutations are also present in the CLEC4f gene in Neanderthals. In contrast to humans, closely related species, including chimpanzees, do have CLEC4f genes that encode full-length receptors. Affinity chromatography and glycan array results demonstrate that the chimpanzee, bovine and murine proteins all bind to galactose, but they show preferences for different subsets of galactose-containing glycans. In non-human primates, the receptor is expressed in spleen rather than in liver. The results indicate that the CLEC4f protein probably has distinct functions in different species. Absence of the receptor precludes using it for targeting of glycoconjugates to cells in human liver. The fact that CLEC4f protein is expressed in spleen in non-human primates and the close evolutionary relationship of the CLEC4f protein to langerin (CD207) suggest that it may function in the immune system, possibly as a pathogen receptor.
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Affiliation(s)
| | - Tom Snelling
- Department of Life Sciences, Imperial College, London, UK
| | - David F Smith
- Emory Comprehensive Glycomics Core, Emory University, Atlanta, GA, USA
| | - Kurt Drickamer
- Department of Life Sciences, Imperial College, London, UK
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172
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Proposed U.S. regulation of gene-edited food animals is not fit for purpose. NPJ Sci Food 2019; 3:3. [PMID: 31304275 PMCID: PMC6550240 DOI: 10.1038/s41538-019-0035-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022] Open
Abstract
Dietary DNA is generally regarded as safe to consume, and is a routine ingredient of food obtained from any living organism. Millions of naturally-occurring DNA variations are observed when comparing the genomic sequence of any two healthy individuals of a given species. Breeders routinely select desired traits resulting from this DNA variation to develop new cultivars and varieties of food plants and animals. Regulatory agencies do not evaluate these new varieties prior to commercial release. Gene editing tools now allow plant and animal breeders to precisely introduce useful genetic variation into agricultural breeding programs. The U.S. Department of Agriculture (USDA) announced that it has no plans to place additional regulations on gene-edited plants that could otherwise have been developed through traditional breeding prior to commercialization. However, the U.S. Food and Drug Administration (FDA) has proposed mandatory premarket new animal drug regulatory evaluation for all food animals whose genomes have been intentionally altered using modern molecular technologies including gene editing technologies. This runs counter to U.S. biotechnology policy that regulatory oversight should be triggered by unreasonable risk, and not by the fact that an organism has been modified by a particular process or technique. Breeder intention is not associated with product risk. Harmonizing the regulations associated with gene editing in food species is imperative to allow both plant and animal breeders access to gene editing tools to introduce useful sustainability traits like disease resistance, climate adaptability, and food quality attributes into U.S. agricultural breeding programs.
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173
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Zhou S, Cai B, He C, Wang Y, Ding Q, Liu J, Liu Y, Ding Y, Zhao X, Li G, Li C, Yu H, Kou Q, Niu W, Petersen B, Sonstegard T, Ma B, Chen Y, Wang X. Programmable Base Editing of the Sheep Genome Revealed No Genome-Wide Off-Target Mutations. Front Genet 2019; 10:215. [PMID: 30930940 PMCID: PMC6428697 DOI: 10.3389/fgene.2019.00215] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/27/2019] [Indexed: 12/23/2022] Open
Abstract
Since its emergence, CRISPR/Cas9-mediated base editors (BEs) with cytosine deaminase activity have been used to precisely and efficiently introduce single-base mutations in genomes, including those of human cells, mice, and crop species. Most production traits in livestock are induced by point mutations, and genome editing using BEs without homology-directed repair of double-strand breaks can directly alter single nucleotides. The p.96R > C variant of Suppressor cytokine signaling 2 (SOCS2) has profound effects on body weight, body size, and milk production in sheep. In the present study, we successfully obtained lambs with defined point mutations resulting in a p.96R > C substitution in SOCS2 by the co-injection of BE3 mRNA and a single guide RNA (sgRNA) into sheep zygotes. The observed efficiency of the single nucleotide exchange in newborn animals was as high as 25%. Observations of body size and body weight in the edited group showed that gene modification contributes to enhanced growth traits in sheep. Moreover, targeted deep sequencing and unbiased family trio-based whole genome sequencing revealed undetectable off-target mutations in the edited animals. This study demonstrates the potential for the application of BE-mediated point mutations in large animals for the improvement of production traits in livestock species.
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Affiliation(s)
- Shiwei Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bei Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chong He
- College of Information Engineering, Northwest A&F University, Yangling, China
| | - Ying Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiang Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yige Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoe Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guanwei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Honghao Yu
- Guilin Medical University, Guilin, China
| | - Qifang Kou
- Ningxia Tianyuan Tan Sheep Farm, Hongsibu, China
| | - Wenzhi Niu
- Ningxia Tianyuan Tan Sheep Farm, Hongsibu, China
| | - Bjoern Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | | | - Baohua Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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174
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Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression. G3-GENES GENOMES GENETICS 2019; 9:359-373. [PMID: 30530642 PMCID: PMC6385975 DOI: 10.1534/g3.118.200810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
One of the most significant physiological challenges to neonatal and juvenile ruminants is the development and establishment of the rumen. Using a subset of RNA-Seq data from our high-resolution atlas of gene expression in sheep (Ovis aries) we have provided the first comprehensive characterization of transcription of the entire gastrointestinal (GI) tract during the transition from pre-ruminant to ruminant. The dataset comprises 164 tissue samples from sheep at four different time points (birth, one week, 8 weeks and adult). Using network cluster analysis we illustrate how the complexity of the GI tract is reflected in tissue- and developmental stage-specific differences in gene expression. The most significant transcriptional differences between neonatal and adult sheep were observed in the rumen complex. Comparative analysis of gene expression in three GI tract tissues from age-matched sheep and goats revealed species-specific differences in genes involved in immunity and metabolism. This study improves our understanding of the transcriptomic mechanisms involved in the transition from pre-ruminant to ruminant by identifying key genes involved in immunity, microbe recognition and metabolism. The results form a basis for future studies linking gene expression with microbial colonization of the developing GI tract and provide a foundation to improve ruminant efficiency and productivity through identifying potential targets for novel therapeutics and gene editing.
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175
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McRae KM, Rowe SJ, Baird HJ, Bixley MJ, Clarke SM. Genome-wide association study of lung lesions and pleurisy in New Zealand lambs. J Anim Sci 2019; 96:4512-4520. [PMID: 30099550 PMCID: PMC6247835 DOI: 10.1093/jas/sky323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022] Open
Abstract
Pneumonia is an important issue for sheep production, leading to reduced growth rate and a predisposition to pleurisy. The objective of this study was to identify loci associated with pneumonic lesions and pleurisy in New Zealand progeny test lambs. The lungs from 3,572 progeny-test lambs were scored for presence and severity of pneumonic lesions and pleurisy at slaughter. Animals were genotyped using the Illumina Ovine Infinium HD SNP BeadChip (606,006 markers). The heritability of lung lesion score and pleurisy were calculated using the genomic relationship matrix, and genome-wide association analyses were conducted using EMMAX and haplotype trend regression. At slaughter, 35% of lambs had pneumonic lesions, with 9% showing lesions on more than half of any individual lobe. The number of lambs recorded as having pleurisy by the processing plants was 9%. Heritability estimates for pneumonic lesions and pleurisy scores adjusted for heteroscedasticity (CPSa and PLEURa) were 0.16 (± 0.03) and 0.05 (± 0.02), respectively. Five single-nucleotide polymorphisms (SNPs) were significantly associated with pneumonic lesions at the genome-wide level, and additional 37 SNPs were suggestively significant. Four SNPs were significantly associated with pleurisy, with an additional 11 SNPs reaching the suggestive level of significance. There were no regions that overlapped between the 2 traits. Multiple SNPs were in regions that contained genes involved in either the DNA damage response or the innate immune response, including several that had previously been reported to have associations with respiratory disease. Both EMMAX and HTR analyses of pleurisy data showed a significant peak on chromosome 2, located downstream from the transcription factor SP3. SP3 activates or suppresses the expression of numerous genes, including several genes with known functions in the immune system. This study identified several SNPs associated with genes involved in both the innate immune response and the response to DNA damage that are associated with pneumonic lesions and pleurisy in lambs at slaughter. Additionally, the identification in sheep of several SNPs within genes that have previously been associated with the respiratory system in cattle, pigs, rats, and mice indicates that there may be common pathways that underlie the response to invasion by respiratory pathogens in multiple species.
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176
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Combined haplotype blocks regression and multi-locus mixed model analysis reveals novel candidate genes associated with milk traits in dairy sheep. Livest Sci 2019. [DOI: 10.1016/j.livsci.2018.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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177
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Jahner JP, Matocq MD, Malaney JL, Cox M, Wolff P, Gritts MA, Parchman TL. The genetic legacy of 50 years of desert bighorn sheep translocations. Evol Appl 2019; 12:198-213. [PMID: 30697334 PMCID: PMC6346675 DOI: 10.1111/eva.12708] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/20/2022] Open
Abstract
Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.
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Affiliation(s)
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental Science, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| | - Jason L. Malaney
- Department of BiologyAustin Peay State UniversityClarksvilleTennessee
| | - Mike Cox
- Nevada Department of Wildlife, and Wild Sheep Working GroupWestern Association of Fish and Wildlife AgenciesRenoNevada
| | | | | | - Thomas L. Parchman
- Department of Biology, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
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178
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Duan JE, Flock K, Jue N, Zhang M, Jones A, Seesi SA, Mandoiu I, Pillai S, Hoffman M, O'Neill R, Zinn S, Govoni K, Reed S, Jiang H, Jiang ZC, Tian XC. Dosage Compensation and Gene Expression of the X Chromosome in Sheep. G3 (BETHESDA, MD.) 2019; 9:305-314. [PMID: 30482800 PMCID: PMC6325915 DOI: 10.1534/g3.118.200815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022]
Abstract
Ohno's hypothesis predicts that the expression of the single X chromosome in males needs compensatory upregulation to balance its dosage with that of the diploid autosomes. Additionally, X chromosome inactivation ensures that quadruple expression of the two X chromosomes is avoided in females. These mechanisms have been actively studied in mice and humans but lag behind in domestic species. Using RNA sequencing data, we analyzed the X chromosome upregulation in sheep fetal tissues from day 135 of gestation under control, over or restricted maternal diets (100%, 140% and 60% of National Research Council Total Digestible Nutrients), and in conceptuses, juvenile, and adult somatic tissues. By computing the mean expression ratio of all X-linked genes to all autosomal genes (X:A), we found that all samples displayed some levels of X chromosome upregulation. The degrees of X upregulation were not significant (P-value = 0.74) between ovine females and males in the same somatic tissues. Brain, however, displayed complete X upregulation. Interestingly, the male and female reproduction-related tissues exhibited divergent X dosage upregulation. Moreover, expression upregulation of the X chromosome in fetal tissues was not affected by maternal diets. Maternal nutrition, however, did change expression levels of several X-linked genes, such as sex determination genes SOX3 and NR0B1 In summary, our results showed that X chromosome upregulation occurred in nearly all sheep somatic tissues analyzed, thus support Ohno's hypothesis in a new species. However, the levels of upregulation differed by different subgroups of genes such as those that are house-keeping and "dosage-sensitive".
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Affiliation(s)
| | | | - Nathanial Jue
- School of Natural Sciences, California State University, Monterey Bay, Seaside, CA 93955
| | - Mingyuan Zhang
- Department of Animal Science
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China
| | | | - Sahar Al Seesi
- Smith College Department of Computer Science, Northampton, MA 01063
- Department of Computer Science
| | | | | | | | - Rachel O'Neill
- Department of Molecular and Cell Biology, and University of Connecticut, Storrs, CT, 06269
| | | | | | | | - Hesheng Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China, and
| | - Zongliang Carl Jiang
- Department of Animal Science
- School of Animal Science, Louisiana State University, Baton Rouge, LA 70803
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179
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Ahbara A, Bahbahani H, Almathen F, Al Abri M, Agoub MO, Abeba A, Kebede A, Musa HH, Mastrangelo S, Pilla F, Ciani E, Hanotte O, Mwacharo JM. Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Front Genet 2019; 9:699. [PMID: 30687385 PMCID: PMC6334744 DOI: 10.3389/fgene.2018.00699] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 12/13/2018] [Indexed: 12/03/2022] Open
Abstract
Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.
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Affiliation(s)
- Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mohammed Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ayelle Abeba
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Hassan Hussein Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, Università Palermo, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “Aldo Moro ”, Bari, Italy
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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180
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Pan Z, Li S, Liu Q, Wang Z, Zhou Z, Di R, Miao B, Hu W, Wang X, Hu X, Xu Z, Wei D, He X, Yuan L, Guo X, Liang B, Wang R, Li X, Cao X, Dong X, Xia Q, Shi H, Hao G, Yang J, Luosang C, Zhao Y, Jin M, Zhang Y, Lv S, Li F, Ding G, Chu M, Li Y. Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization. Gigascience 2018; 7:4924504. [PMID: 29668959 PMCID: PMC5905515 DOI: 10.1093/gigascience/giy019] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 02/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background Animal domestication has been extensively studied, but the process of feralization remains poorly understood. Results Here, we performed whole-genome sequencing of 99 sheep and identified a primary genetic divergence between 2 heterogeneous populations in the Tibetan Plateau, including 1 semi-feral lineage. Selective sweep and candidate gene analysis revealed local adaptations of these sheep associated with sensory perception, muscle strength, eating habit, mating process, and aggressive behavior. In particular, a horn-related gene, RXFP2, showed signs of rapid evolution specifically in the semi-feral breeds. A unique haplotype and repressed horn-related tissue expression of RXFP2 were correlated with higher horn length, as well as spiral and horizontally extended horn shape. Conclusions Semi-feralization has an extensive impact on diverse phenotypic traits of sheep. By acquiring features like those of their wild ancestors, semi-feral sheep were able to regain fitness while in frequent contact with wild surroundings and rare human interventions. This study provides a new insight into the evolution of domestic animals when human interventions are no longer dominant.
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Affiliation(s)
- Zhangyuan Pan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Shengdi Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiuyue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Benpeng Miao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenping Hu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoxiang Hu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Ze Xu
- BasePair BioTechonology Co., Ltd., Suzhou, China
| | - Dongkai Wei
- BasePair BioTechonology Co., Ltd., Suzhou, China
| | - Xiaoyun He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyun Yuan
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaofei Guo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Benmeng Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruichao Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyu Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohan Cao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinlong Dong
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing Xia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongcai Shi
- Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, China
| | - Geng Hao
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
| | - Jean Yang
- Research Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Cuicheng Luosang
- Research Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yiqiang Zhao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Mei Jin
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Yingjie Zhang
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China
| | - Shenjin Lv
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Fukuan Li
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Guohui Ding
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China
| | - Mingxing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China
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181
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Zhang Z, Jia Y, Almeida P, Mank JE, van Tuinen M, Wang Q, Jiang Z, Chen Y, Zhan K, Hou S, Zhou Z, Li H, Yang F, He Y, Ning Z, Yang N, Qu L. Whole-genome resequencing reveals signatures of selection and timing of duck domestication. Gigascience 2018; 7:4965113. [PMID: 29635409 PMCID: PMC6007426 DOI: 10.1093/gigascience/giy027] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/18/2018] [Indexed: 12/28/2022] Open
Abstract
Background The genetic basis of animal domestication remains poorly understood, and systems with
substantial phenotypic differences between wild and domestic populations are useful for
elucidating the genetic basis of adaptation to new environments as well as the genetic
basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual
ducks, from two wild and seven domesticated populations, with an average sequencing
depth of 6.42X per individual. Results Our population and demographic analyses indicate a complex history of domestication,
with early selection for separate meat and egg lineages. Genomic comparison of wild to
domesticated populations suggests that genes that affect brain and neuronal development
have undergone strong positive selection during domestication. Our FST
analysis also indicates that the duck white plumage is the result of selection at the
melanogenesis-associated transcription factor locus. Conclusions Our results advance the understanding of animal domestication and selection for complex
phenotypic traits.
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Affiliation(s)
- Zebin Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pedro Almeida
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Marcel van Tuinen
- Centre of Evolutionary and Ecological Studies, Marine Evolution and Conservation Group, University of Groningen, Groningen, The Netherlands
| | - Qiong Wang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhihua Jiang
- Department of Animal Sciences, Center for Reproductive Biology, Veterinary and Biomedical Research Building, Washington State University, Pullman, United States
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Kai Zhan
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shuisheng Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huifang Li
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, China
| | | | - Yong He
- Cherry Valley farms (xianghe) Co., Ltd, Langfang, China
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Morrison JL, Berry MJ, Botting KJ, Darby JRT, Frasch MG, Gatford KL, Giussani DA, Gray CL, Harding R, Herrera EA, Kemp MW, Lock MC, McMillen IC, Moss TJ, Musk GC, Oliver MH, Regnault TRH, Roberts CT, Soo JY, Tellam RL. Improving pregnancy outcomes in humans through studies in sheep. Am J Physiol Regul Integr Comp Physiol 2018; 315:R1123-R1153. [PMID: 30325659 DOI: 10.1152/ajpregu.00391.2017] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Experimental studies that are relevant to human pregnancy rely on the selection of appropriate animal models as an important element in experimental design. Consideration of the strengths and weaknesses of any animal model of human disease is fundamental to effective and meaningful translation of preclinical research. Studies in sheep have made significant contributions to our understanding of the normal and abnormal development of the fetus. As a model of human pregnancy, studies in sheep have enabled scientists and clinicians to answer questions about the etiology and treatment of poor maternal, placental, and fetal health and to provide an evidence base for translation of interventions to the clinic. The aim of this review is to highlight the advances in perinatal human medicine that have been achieved following translation of research using the pregnant sheep and fetus.
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Affiliation(s)
- Janna L Morrison
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Mary J Berry
- Department of Paediatrics and Child Health, University of Otago , Wellington , New Zealand
| | - Kimberley J Botting
- Department of Physiology, Development, and Neuroscience, University of Cambridge , Cambridge , United Kingdom
| | - Jack R T Darby
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Martin G Frasch
- Department of Obstetrics and Gynecology, University of Washington , Seattle, Washington
| | - Kathryn L Gatford
- Robinson Research Institute and Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Dino A Giussani
- Department of Physiology, Development, and Neuroscience, University of Cambridge , Cambridge , United Kingdom
| | - Clint L Gray
- Department of Paediatrics and Child Health, University of Otago , Wellington , New Zealand
| | - Richard Harding
- Department of Anatomy and Developmental Biology, Monash University , Clayton, Victoria , Australia
| | - Emilio A Herrera
- Pathophysiology Program, Biomedical Sciences Institute (ICBM), Faculty of Medicine, University of Chile , Santiago , Chile
| | - Matthew W Kemp
- Division of Obstetrics and Gynecology, University of Western Australia , Perth, Western Australia , Australia
| | - Mitchell C Lock
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - I Caroline McMillen
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Timothy J Moss
- The Ritchie Centre, Hudson Institute of Medical Research, Department of Obstetrics and Gynaecology, Monash University , Clayton, Victoria , Australia
| | - Gabrielle C Musk
- Animal Care Services, University of Western Australia , Perth, Western Australia , Australia
| | - Mark H Oliver
- Liggins Institute, University of Auckland , Auckland , New Zealand
| | - Timothy R H Regnault
- Department of Obstetrics and Gynecology and Department of Physiology and Pharmacology, Western University, and Children's Health Research Institute , London, Ontario , Canada
| | - Claire T Roberts
- Robinson Research Institute and Adelaide Medical School, University of Adelaide , Adelaide, South Australia , Australia
| | - Jia Yin Soo
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Ross L Tellam
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
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184
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Chen ZH, Zhang M, Lv FH, Ren X, Li WR, Liu MJ, Nam K, Bruford MW, Li MH. Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species. Genome Biol Evol 2018; 10:1282-1297. [PMID: 29790980 PMCID: PMC5963296 DOI: 10.1093/gbe/evy085] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2018] [Indexed: 01/08/2023] Open
Abstract
Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05–79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep’s recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.
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Affiliation(s)
- Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xue Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Kiwoong Nam
- Diversité, Génomes et Interactions Microorganismes Insectes, Institut National de la Recherche Agronomique, University of Montpellier, Montpellier, France
| | - Michael W Bruford
- Organisms and Environment Division, School of Biosciences and Sustainable Places Research Institute, Cardiff University, Wales, United Kingdom
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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185
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Giuffra E, Tuggle CK. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annu Rev Anim Biosci 2018; 7:65-88. [PMID: 30427726 DOI: 10.1146/annurev-animal-020518-114913] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.
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Affiliation(s)
- Elisabetta Giuffra
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France;
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186
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Patil RD, Ellison MJ, Wolff SM, Shearer C, Wright AM, Cockrum RR, Austin KJ, Lamberson WR, Cammack KM, Conant GC. Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes. J Anim Sci 2018; 96:2113-2124. [PMID: 29788417 DOI: 10.1093/jas/sky096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/14/2018] [Indexed: 12/19/2022] Open
Abstract
Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.
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Affiliation(s)
- Rocky D Patil
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO
| | - Melinda J Ellison
- Animal and Veterinary Science, Nancy M. Cummings Research, Extension, and Education Center, University of Idaho, Carmen, ID
| | - Sara M Wolff
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO
| | | | - Anna M Wright
- Department of Psychological Sciences, University of Missouri-Columbia, Columbia, MO
| | - Rebecca R Cockrum
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Kathy J Austin
- Department of Animal Science, University of Wyoming, Laramie, WY
| | | | - Kristi M Cammack
- Department of Animal Science, South Dakota State University, Brookings, SD
| | - Gavin C Conant
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO.,Program in Genetics, North Carolina State University, Raleigh, NC.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC.,Department of Biological Sciences, North Carolina State University, Raleigh, NC
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187
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Yang Y, Wang Y, Zhao Y, Zhang X, Li R, Chen L, Zhang G, Jiang Y, Qiu Q, Wang W, Wei HJ, Wang K. Draft genome of the Marco Polo Sheep (Ovis ammon polii). Gigascience 2018; 6:1-7. [PMID: 29112761 PMCID: PMC5740985 DOI: 10.1093/gigascience/gix106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/30/2017] [Indexed: 11/14/2022] Open
Abstract
Background The Marco Polo Sheep (Ovis ammon polii), a subspecies of argali (Ovis ammon) that is distributed mainly in the Pamir Mountains, provides a mammalian model to study high altitude adaptation mechanisms. Due to over-hunting and subsistence poaching, as well as competition with livestock and habitat loss, O. ammon has been categorized as an endangered species on several lists. It can have fertile offspring with sheep. Hence, a high-quality reference genome of the Marco Polo Sheep will be very helpful in conservation genetics and even in exploiting useful genes in sheep breeding. Findings A total of 1022.43 Gb of raw reads resulting from whole-genome sequencing of a Marco Polo Sheep were generated using an Illumina HiSeq2000 platform. The final genome assembly (2.71 Gb) has an N50 contig size of 30.7 Kb and a scaffold N50 of 5.49 Mb. The repeat sequences identified account for 46.72% of the genome, and 20 336 protein-coding genes were predicted from the masked genome. Phylogenetic analysis indicated a close relationship between Marco Polo Sheep and the domesticated sheep, and the time of their divergence was approximately 2.36 million years ago. We identified 271 expanded gene families and 168 putative positively selected genes in the Marco Polo Sheep lineage. Conclusions We provide the first genome sequence and gene annotation for the Marco Polo Sheep. The availability of these resources will be of value in the future conservation of this endangered large mammal, for research into high altitude adaptation mechanisms, for reconstructing the evolutionary history of the Caprinae, and for the future conservation of the Marco Polo Sheep.
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Affiliation(s)
- Yongzhi Yang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yutao Wang
- College of Life and Geographic Sciences, Kashgar University, Kashgar 844000, China.,The Key Laboratory of Ecology and Biological Resources in Yark and Oasis at Colleges and Universities under the Department of Education of Xinjiang Uygur Autonomous Region, Kashgar University, Kashgar 844000, China
| | - Yue Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiuying Zhang
- College of Life and Geographic Sciences, Kashgar University, Kashgar 844000, China.,The Key Laboratory of Ecology and Biological Resources in Yark and Oasis at Colleges and Universities under the Department of Education of Xinjiang Uygur Autonomous Region, Kashgar University, Kashgar 844000, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen 2100, Denmark
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Qiang Qiu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Hong-Jiang Wei
- Key Laboratory Animal Nutrition and Feed of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
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188
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Pan Z, Wang X, Di R, Liu Q, Hu W, Cao X, Guo X, He X, Lv S, Li F, Wang H, Chu M. A 5-Methylcytosine Site of Growth Differentiation Factor 9 (GDF9) Gene Affects Its Tissue-Specific Expression in Sheep. Animals (Basel) 2018; 8:ani8110200. [PMID: 30405007 PMCID: PMC6262488 DOI: 10.3390/ani8110200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/21/2018] [Accepted: 10/24/2018] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Growth differentiation factor 9 (GDF9) is an important gene for ovine fertility. GDF9 is highly expressed in the ovary as opposed to other tissues, but the reason for this is unknown. Our study found this can be caused by the methylation level of the promoter CpG island mC-4 site. This finding contributes to the understanding of the regulatory mechanism of GDF9 gene in reproduction. Abstract Growth differentiation factor 9 (GDF9) plays an important role in the early folliculogenesis of sheep. This study investigated the mRNA expression of ovine GDF9 in different tissues by real-time PCR. GDF9 exhibits significantly higher levels of expression (p < 0.01) in the ovary, relative to other tissues, indicating that its expression is tissue specific. To explore the regulatory mechanism of this tissue-specific expression, the methylation level of one CpG island (−1453 to −1854) of GDF9 promoter in ovary and heart was determined. In this region (−1987 to −1750), only the mC-4 site was present in the Sp4 binding site showed differential methylation between the heart and ovary; with increased (p < 0.01) methylation being observed in the heart. Additionally, the methylation level was negatively correlated with GDF9 mRNA expression (R = −0.75, p = 0.012), indicating that the methylation of this site plays an important role in transcriptional regulation of GDF9. The methylation effect of the mC-4 site was confirmed by using dual-luciferase. Site-directed mutation (methylation) of mC-4 site significantly reduced (p < 0.05) basal transcriptional activity of GDF9 promoter in oocytes. These results imply that methylation of GDF9 promoter CpG island mC-4 site may affect the binding of the Sp4 transcription factor to the GDF9 promoter region in sheep, thereby regulating GDF9 expression and resulting in a tissue-specific expression.
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Affiliation(s)
- Zhangyuan Pan
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- College of Agriculture and Forestry Science, Linyi University, Linyi 276000, China.
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Qiuyue Liu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Wenping Hu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaohan Cao
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaofei Guo
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaoyun He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengjin Lv
- College of Agriculture and Forestry Science, Linyi University, Linyi 276000, China.
| | - Fukuan Li
- College of Agriculture and Forestry Science, Linyi University, Linyi 276000, China.
| | - Hui Wang
- College of Agriculture and Forestry Science, Linyi University, Linyi 276000, China.
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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189
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O’Connor RE, Farré M, Joseph S, Damas J, Kiazim L, Jennings R, Bennett S, Slack EA, Allanson E, Larkin DM, Griffin DK. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol 2018; 19:171. [PMID: 30355328 PMCID: PMC6201548 DOI: 10.1186/s13059-018-1550-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/24/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. RESULTS We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest. CONCLUSIONS The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.
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Affiliation(s)
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Lucas Kiazim
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Sophie Bennett
- School of Biosciences, University of Kent, Canterbury, UK
| | - Eden A Slack
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Emily Allanson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK
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190
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Leiberich M, Marais HJ, Naidoo V. Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros ( Ceratotherium simum) and other mammalian species. PeerJ 2018; 6:e5718. [PMID: 30324017 PMCID: PMC6183514 DOI: 10.7717/peerj.5718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/08/2018] [Indexed: 01/08/2023] Open
Abstract
Background The plight of the white rhinoceros (Ceratotherium simum) and the increasing need of treatment options for injured poaching victims led to the necessity to expand the knowledge on applicable drugs in this endangered species. With very little information available on drug pharmacokinetics in rhino, veterinarians have to rely on information generated from other species. The horse being a closely related species, has served as the model for dose extrapolations. However, from recent research on enrofloxacin and carprofen, the white rhino showed considerable differences in the pharmacokinetic properties of these drugs in comparison to the horse. While the reason for the differences is unknown, a likely cause may be a difference in present cytochrome P450 (CYP450), which may result in the rhino being genetically deficient in certain enzyme families. Methods For this paper we assess the degree of similarity of the CYP genome sequences across the different species, using BLAT (BLAST-like alignment tool) for the alignment of the nucleotide sequences of the equine CYP450 with potential homologous nucleotide sequences of the published database from white rhinos and other mammalian species (cow, pig, dog, sheep, elephant, mouse and human). Results The white rhino nucleotide sequences were 90.74% identical to the equine sequences. This was higher than the degree of similarity between any of the other evaluated species sequences. While no specific CYP family were found to be deficient in the published rhino genome, the horse genome contained additional genetic sequence for a larger number of iso-enzymes that were not present in the rhino. Discussion In pharmacokinetic study, it is well known that absence of a metabolic enzyme will result in constraints in drug metabolism and drug elimination. While this was our speculation, comparison to the horse and other mammalian species indicate that all the described CYP genes required for metabolism are present within the rhino genome. These results leave functional differences in enzyme activity and a lack of isoenzymes as the likely reason for the constraint in drug metabolism. Despite a more than 90% similarity of the equine and rhino gene sequences, seemingly small differences can have major effects on drug metabolism. Thus, in spite of the close anatomical relationship, the rhino should not simply be treated like a big horse.
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Affiliation(s)
- Marion Leiberich
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | | | - Vinny Naidoo
- Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
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191
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Mitchell NL, Russell KN, Wellby MP, Wicky HE, Schoderboeck L, Barrell GK, Melzer TR, Gray SJ, Hughes SM, Palmer DN. Longitudinal In Vivo Monitoring of the CNS Demonstrates the Efficacy of Gene Therapy in a Sheep Model of CLN5 Batten Disease. Mol Ther 2018; 26:2366-2378. [PMID: 30078766 PMCID: PMC6171082 DOI: 10.1016/j.ymthe.2018.07.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 07/08/2018] [Accepted: 07/12/2018] [Indexed: 02/03/2023] Open
Abstract
Neuronal ceroid lipofuscinoses (NCLs; Batten disease) are neurodegenerative lysosomal storage diseases predominantly affecting children. Single administration of brain-directed lentiviral or recombinant single-stranded adeno-associated virus 9 (ssAAV9) vectors expressing ovine CLN5 into six pre-clinically affected sheep with a naturally occurring CLN5 NCL resulted in long-term disease attenuation. Treatment efficacy was demonstrated by non-invasive longitudinal in vivo monitoring developed to align with assessments used in human medicine. The treated sheep retained neurological and cognitive function, and one ssAAV9-treated animal has been retained and is now 57 months old, almost triple the lifespan of untreated CLN5-affected sheep. The onset of visual deficits was much delayed. Computed tomography and MRI showed that brain structures and volumes remained stable. Because gene therapy in humans is more likely to begin after clinical diagnosis, self-complementary AAV9-CLN5 was injected into the brain ventricles of four 7-month-old affected sheep already showing early clinical signs in a second trial. This also halted disease progression beyond their natural lifespan. These findings demonstrate the efficacy of CLN5 gene therapy, using three different vector platforms, in a large animal model and, thus, the prognosis for human translation.
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Affiliation(s)
- Nadia L Mitchell
- Department of Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; Department of Radiology, University of Otago, Christchurch 8140, New Zealand
| | - Katharina N Russell
- Department of Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Martin P Wellby
- Department of Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Hollie E Wicky
- Department of Biochemistry, Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand
| | - Lucia Schoderboeck
- Department of Biochemistry, Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand
| | - Graham K Barrell
- Department of Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Tracy R Melzer
- Department of Medicine, University of Otago, Christchurch 8140, New Zealand
| | - Steven J Gray
- Gene Therapy Center and Department of Ophthalmology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephanie M Hughes
- Department of Biochemistry, Brain Health Research Centre, University of Otago, Dunedin 9054, New Zealand
| | - David N Palmer
- Department of Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; Department of Radiology, University of Otago, Christchurch 8140, New Zealand.
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192
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Goudet J, Kay T, Weir BS. How to estimate kinship. Mol Ecol 2018; 27:4121-4135. [PMID: 30107060 PMCID: PMC6220858 DOI: 10.1111/mec.14833] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023]
Abstract
The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next‐generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker‐based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.
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Affiliation(s)
- Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Tomas Kay
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, Washington
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193
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Dardente H, Lomet D. Photoperiod and thyroid hormone regulate expression of l-dopachrome tautomerase (Dct), a melanocyte stem-cell marker, in tanycytes of the ovine hypothalamus. J Neuroendocrinol 2018; 30:e12640. [PMID: 30129070 DOI: 10.1111/jne.12640] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/16/2018] [Indexed: 12/16/2022]
Abstract
The pars tuberalis (PT) of the pituitary is central to the control of seasonal breeding. In mammals, the PT translates the photoperiodic message carried by melatonin into an endocrine thyroid-stimulating hormone output, which controls local thyroid hormone (TH) signalling in tanycytes of the neighbouring hypothalamus. In the present study, we identify l-dopachrome tautomerase (Dct) as a novel marker of ovine tanycytes and show that Dct displays marked seasonal variations in expression, with higher levels during spring and summer. This seasonal profile is photoperiod-dependent because an acute exposure to long days induces Dct expression. In addition, we find that TH also modulates Dct expression. DCT functions as an enzyme in the melanin synthesis pathway within skin melanocytes, whereas expression in other tissues is comparatively low. We demonstrate that both Tyr and Tyrp1, which are enzymes that intervene upstream and downstream of Dct in the melanin synthesis pathway, respectively, are expressed at very low levels in the ovine hypothalamus. This suggests that Dct in tanycytes may not be involved in melanin synthesis. We speculate that DCT function is linked to its protective role towards oxidative stress and/or its function in the control of neural progenitor cell proliferation.
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Affiliation(s)
- Hugues Dardente
- PRC, INRA, CNRS, IFCE, Université de Tours, Nouzilly, France
| | - Didier Lomet
- PRC, INRA, CNRS, IFCE, Université de Tours, Nouzilly, France
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194
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Comparing polymorphism of 86 candidate genes putatively involved in domestication of sheep, between wild and domestic Iranian sheep. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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195
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Tenascin-XB (TNXB) amino acid substitution E2004G is associated with mature weight and milk score in American Rambouillet, Targhee, Polypay, and Suffolk sheep. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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196
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Endo Y, Kamei KI, Inoue-Murayama M. Genetic signatures of lipid metabolism evolution in Cetacea since the divergence from terrestrial ancestor. J Evol Biol 2018; 31:1655-1665. [DOI: 10.1111/jeb.13361] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/12/2018] [Accepted: 07/28/2018] [Indexed: 12/25/2022]
Affiliation(s)
| | - Ken-ichiro Kamei
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Kyoto Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center; Kyoto University; Kyoto Japan
- Wildlife Genome Collaborative Research Group; National Institute for Environmental Studies; Tsukuba Ibaraki Japan
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197
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Xiang R, McNally J, Bond J, Tucker D, Cameron M, Donaldson AJ, Austin KL, Rowe S, Jonker A, Pinares-Patino CS, McEwan JC, Vercoe PE, Oddy VH, Dalrymple BP. Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes. Front Genet 2018; 9:330. [PMID: 30177952 PMCID: PMC6109778 DOI: 10.3389/fgene.2018.00330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/31/2018] [Indexed: 01/03/2023] Open
Abstract
Ruminants are significant contributors to the livestock generated component of the greenhouse gas, methane (CH4). The CH4 is primarily produced by the rumen microbes. Although the composition of the diet and animal intake amount have the largest effect on CH4 production and yield (CH4 production/dry matter intake, DMI), the host also influences CH4 yield. Shorter rumen feed mean retention time (MRT) is associated with higher dry matter intake and lower CH4 yield, but the molecular mechanism(s) by which the host affects CH4 production remain unclear. We integrated rumen wall transcriptome data and CH4 phenotypes from two independent experiments conducted with sheep in Australia (AUS, n = 62) and New Zealand (NZ, n = 24). The inclusion of the AUS data validated the previously identified clusters and gene sets representing rumen epithelial, metabolic and muscular functions. In addition, the expression of the cell cycle genes as a group was consistently positively correlated with acetate and butyrate concentrations (p < 0.05, based on AUS and NZ data together). The expression of a group of metabolic genes showed positive correlations in both AUS and NZ datasets with CH4 production (p < 0.05) and yield (p < 0.01). These genes encode key enzymes in the ketone body synthesis pathway and included members of the poorly characterized aldo-keto reductase 1C (AKR1C) family. Several AKR1C family genes appear to have ruminant specific evolution patterns, supporting their specialized roles in the ruminants. Combining differential gene expression in the rumen wall muscle of the shortest and longest MRT AUS animals (no data available for the NZ animals) with correlation and network analysis, we identified a set of rumen muscle genes involved in cell junctions as potential regulators of MRT, presumably by influencing contraction rates of the smooth muscle component of the rumen wall. Higher rumen expression of these genes, including SYNPO (synaptopodin, p < 0.01) and NEXN (nexilin, p < 0.05), was associated with lower CH4 yield in both AUS and NZ datasets. Unlike the metabolic genes, the variations in the expression of which may reflect the availability of rumen metabolites, the muscle genes are currently our best candidates for causal genes that influence CH4 yield.
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Affiliation(s)
- Ruidong Xiang
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Jody McNally
- F. D. McMaster Laboratory, CSIRO Agriculture & Food, Armidale, NSW, Australia
| | - Jude Bond
- NSW Department of Primary Industries, Extensive Livestock Industries Centre, University of New England, Armidale, NSW, Australia
| | - David Tucker
- NSW Department of Primary Industries, Extensive Livestock Industries Centre, University of New England, Armidale, NSW, Australia
| | - Margaret Cameron
- NSW Department of Primary Industries, Extensive Livestock Industries Centre, University of New England, Armidale, NSW, Australia
| | - Alistair J Donaldson
- NSW Department of Primary Industries, Extensive Livestock Industries Centre, University of New England, Armidale, NSW, Australia
| | - Katie L Austin
- NSW Department of Primary Industries, Extensive Livestock Industries Centre, University of New England, Armidale, NSW, Australia
| | - Suzanne Rowe
- Invermay Agricultural Centre, AgResearch Limited, Mosgiel, New Zealand
| | - Arjan Jonker
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Cesar S Pinares-Patino
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand.,New Zealand-Peru Dairy Support Project, MINAGRI, Lima, Peru
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch Limited, Mosgiel, New Zealand
| | - Phil E Vercoe
- School of Animal Biology, The University of Western Australia, Crawley, WA, Australia.,Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - V H Oddy
- NSW Department of Primary Industries, Extensive Livestock Industries Centre, University of New England, Armidale, NSW, Australia
| | - Brian P Dalrymple
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia.,Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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198
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Global genomic diversity and conservation priorities for domestic animals are associated with the economies of their regions of origin. Sci Rep 2018; 8:11677. [PMID: 30076315 PMCID: PMC6076285 DOI: 10.1038/s41598-018-30061-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/18/2018] [Indexed: 12/03/2022] Open
Abstract
Domestic animals play a key role in human survival and the development of civilization. However, the genetic resources of domestic animals are facing an alarming rate of erosion due to socioeconomic changes, economic globalization and financial constraints. In this study, through genome-wide SNP analysis, we estimated the heterozygosity, inbreeding coefficient, effective population size, and runs of homozygosity to identify the breeds facing the risk of extinction for sheep and cattle across the world. In particular, we quantified the contribution of 97 sheep breeds and 53 cattle breeds to genomic diversity (within-breed, between-breed and total) and prioritized the breeds for conservation. Additionally, we compared the average values of genomic diversity between breeds from regions (or countries) in different economic categories (underdeveloped, developing and developed), and found that breeds in developed regions exhibit significantly higher levels of total genomic diversity than those in underdeveloped and developing regions. Altogether, our results suggested that conservation priority should be given to breeds in developed regions to secure the future genomic diversity hotspots of domestic animal resources.
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199
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Tang Q, Gu Y, Zhou X, Jin L, Guan J, Liu R, Li J, Long K, Tian S, Che T, Hu S, Liang Y, Yang X, Tao X, Zhong Z, Wang G, Chen X, Li D, Ma J, Wang X, Mai M, Jiang A, Luo X, Lv X, Gladyshev VN, Li X, Li M. Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives. Gigascience 2018; 6:1-9. [PMID: 29149296 PMCID: PMC5729692 DOI: 10.1093/gigascience/gix105] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 10/24/2017] [Indexed: 01/22/2023] Open
Abstract
Background Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. Findings We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression-based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. Conclusions These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments.
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Affiliation(s)
- Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiuqiang Guan
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Rui Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kereng Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Guosong Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Department of Animal Science, Texas A & M University, College Station, Texas, 77843 USA
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Miaomiao Mai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - An'an Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolin Luo
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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200
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Li S, Luo R, Lai D, Ma M, Hao F, Qi X, Liu X, Liu D. Whole-genome resequencing of Ujumqin sheep to investigate the determinants of the multi-vertebral trait. Genome 2018; 61:653-661. [PMID: 30001497 DOI: 10.1139/gen-2017-0267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Ujumqin sheep is one of the most profitable breeds in China, with unique multi-vertebral characteristics. We performed high-throughput genome resequencing of five multi-vertebral and three non-multi-vertebral sheep in an Ujumqin population. We identified the genomic regions that correlated with the germplasm characteristics to establish the cause of the "multi-vertebral" phenotype in this breed. Sequencing generated a total of 314 952 000 000 bp of raw data. The alignment rate of all the samples was between 98.53% and 99.11%, and the mean depth of coverage relative to the reference genome was between 11.58× and 14.92×. After comparing the differences between the two groups, we identified 21 homozygous single nucleotide polymorphisms (SNPs) in the mutant exons of 14 genes. Nineteen loci of 10 genes contained nonsynonymous mutations, while two loci contained synonymous mutations. Resequencing revealed homozygous mutations comprised of 44 indels located within exons of 19 genes. These indels included 37 frameshift mutations, 6 non-frameshift mutations, and 1 stopgain single nucleotide variation (SNV). Finally, comparisons of genotypic variations revealed 17 genes with homozygous mutations in their coding regions, 5 of which have previously been associated with vertebral development and the remaining 12 genes were newly identified in this study.
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Affiliation(s)
- Shuo Li
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
| | - Rongsong Luo
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
| | - Defang Lai
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
| | - Min Ma
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
| | - Fei Hao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
| | - Xuan Qi
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
| | - Xu Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
| | - Dongjun Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China.,State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Inner Mongolia, Hohhot, 010070, P.R. China
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